The global financial crisis wiped £1.3bn from the value of the Church of England's asset portfolio, according to accounts publishedyesterday. The church's annual financial report revealed the portfolio had fallen to £4.4bn, its lowest since 2004.

The Church Commissioners' funds had been predicted to fall even further, although similar funds have performed slightly better.

Andrew Brown, secretary to the commissioners, put a brave face on the figures. "We have money tied up in property and equities and all our investment markets were hit last year, with the exception of government securities and gilts and we don't have many of those," said Brown. "Our assets are real – that is they increase in value or they go down – because our liabilities increase."

The biggest expense of the fund is more than £100m in annual pension payments to retired clergy.

Brown said churches would not have to go without. "The fact that we had already sold £300m of equities and £400m of residential property, when the markets were much higher, and the fact that we have the smoothing mechanism, which allows us to hold money back, means we've been preparing ourselves."

The organisation is responsible for managing the historic property assets of the Church of England. It contributes around 17% towards the Church of England's running costs, which is more than £1.1bn a year. Parishioners pay the outstanding amount.

Earlier this year the Archbishop of Canterbury, Rowan Williams, used a lecture in Cardiff to deliver a wide-ranging attack on a globalised economic system which had been "spectacularly successful in generating purchasing power", but which had also led people to "the most radical insecurity imaginable".

He criticised the unthinking pursuit of growth, which he said had led to an unhealthily hyperactive economy.

The Archbishop of York, John Sentamu, has gone further, calling share traders who cashed in on falling prices "bank robbers and asset strippers".

It subsequently emerged that the Church Commissioners may have profited from the practice, known as short selling, when a thinktank claimed that the body had set up a currency hedging programme in 2006, in effect short-selling sterling to guard against rises in other currencies. The organisation denied the charge.